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Aktürk Dizman Y. Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes. J Basic Microbiol 2024; 64:e2400289. [PMID: 39099168 DOI: 10.1002/jobm.202400289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/05/2024] [Accepted: 07/20/2024] [Indexed: 08/06/2024]
Abstract
Ranaviruses, members of the genus Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of Ranavirus to its hosts.
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Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, Rize, Türkiye
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Hartmann A, Subramaniam K, Conrad C, Viadanna PHO, Waltzek TB, Longo AV. Genomic characterization of two ranavirus isolates identified from a gopher frog ( Lithobates capito) and a striped newt ( Notophthalmus perstriatus) during a mass mortality event in Florida. Microbiol Resour Announc 2024; 13:e0001724. [PMID: 38651908 PMCID: PMC11237735 DOI: 10.1128/mra.00017-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Two ranavirus isolates were recovered from anuran and salamander samples collected during an amphibian mass mortality event in North-Central Florida in 2021. Phylogenetic analyses of the full genomes confirmed that the two isolates were nearly identical and strains of the species Frog virus 3.
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Affiliation(s)
- Arik Hartmann
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Cody Conrad
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Pedro H O Viadanna
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Veterinary Microbiology and Pathology, Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Ana V Longo
- Department of Biology, University of Florida, Gainesville, Florida, USA
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McGrath-Blaser SE, McGathey N, Pardon A, Hartmann AM, Longo AV. Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens. Proc Biol Sci 2024; 291:20232658. [PMID: 38628130 PMCID: PMC11021929 DOI: 10.1098/rspb.2023.2658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
North American salamanders are threatened by intercontinental spread of chytridiomycosis, a deadly disease caused by the fungal pathogen Batrachochytrium salamandrivorans (Bsal). To predict potential dispersal of Bsal spores to salamander habitats, we evaluated the capacity of soil microbial communities to resist invasion. We determined the degree of habitat invasibility using soils from five locations throughout the Great Smoky Mountains National Park, a region with a high abundance of susceptible hosts. Our experimental design consisted of replicate soil microcosms exposed to different propagule pressures of the non-native pathogen, Bsal, and an introduced but endemic pathogen, B. dendrobatidis (Bd). To compare growth and competitive interactions, we used quantitative PCR, live/dead cell viability assays, and full-length 16S rRNA sequencing. We found that soil microcosms with intact bacterial communities inhibited both Bsal and Bd growth, but inhibitory capacity diminished with increased propagule pressure. Bsal showed greater persistence than Bd. Linear discriminant analysis (LDA) identified the family Burkolderiaceae as increasing in relative abundance with the decline of both pathogens. Although our findings provide evidence of environmental filtering in soils, such barriers weakened in response to pathogen type and propagule pressure, showing that habitats vary their invasibility based on properties of their local microbial communities.
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Affiliation(s)
| | - Natalie McGathey
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Allison Pardon
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Arik M. Hartmann
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ana V. Longo
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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Hartmann AM, McGrath-Blaser SE, Colón-Piñeiro Z, Longo AV. Ontogeny drives shifts in skin bacterial communities in facultatively paedomorphic salamanders. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001399. [PMID: 37815535 PMCID: PMC10634365 DOI: 10.1099/mic.0.001399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/02/2023] [Indexed: 10/11/2023]
Abstract
Microbiomes are major determinants of host growth, development and survival. In amphibians, host-associated bacteria in the skin can inhibit pathogen infection, but many processes can influence the structure and composition of the community. Here we quantified the shifts in skin-associated bacteria across developmental stages in the striped newt (Notophthalmus perstriatus), a threatened salamander species with a complex life history and vulnerable to infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis and ranavirus. Our analyses show that pre-metamorphic larval and paedomorphic stages share similar bacterial compositions, and that the changes in the microbiome coincided with physiological restructuring during metamorphosis. Newts undergoing metamorphosis exhibited microbiome compositions that were intermediate between paedomorphic and post-metamorphic stages, further supporting the idea that metamorphosis is a major driver of host-associated microbes in amphibians. We did not find support for infection-related disruption of the microbiome, though infection replicates were small for each respective life stage.
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Affiliation(s)
- Arik M. Hartmann
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | | | - Ana V. Longo
- Department of Biology, University of Florida, Gainesville, Florida, USA
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Pastorino P, Colussi S, Varello K, Meletiadis A, Alberti S, Di Blasio A, Tedde G, Begovoeva M, Peano A, Rossi L, Renzi M, Acutis PL, Barceló D, Prearo M. Interdisciplinary approach to solve unusual mortalities in the European common frog (Rana temporaria) in two high-mountain ponds affected by climate change. ENVIRONMENTAL RESEARCH 2023; 222:115411. [PMID: 36736753 DOI: 10.1016/j.envres.2023.115411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
The global decline in amphibian populations is a major environmental issue. Chytridiomycosis, Ranaviruses and the red-leg syndrome have been identified in unusual mortality events. However, these infections do not account for all causes of declining amphibian populations. Moreover, several cases of amphibian mortality are difficult to solve without resorting to an interdisciplinary approach. Two cases of unusual mortality in Rana temporaria occurred at two high-mountain ponds (northwest Italy) in April and May 2021. Water and frog samples were analysed to understand the possible causes responsible for the unusual mortalities. Results of the main physicochemical (pH, conductivity, dissolved oxygen, chemical and biochemical oxygen demand) and nutrient (ammonia/ammonium, nitrite, nitrate, total phosphorus) parameters revealed a good condition of the water quality, with the absence of the main cyanotoxins (microcystins/nodularins). However, unseasonably high spring water temperatures were recorded in both ponds (12.73 °C and 14.21 °C for Frog Pond and Selleries Pond, respectively). Frogs (n = 50; snout-vent length: 7.0-9.8 cm; body mass: 85-123 g) collected from Frog Pond mainly presented bumps on the ventral cavity and dermal ulceration associated with the isolation of Carnobacterium maltaromaticum. On the other hand, frogs (n = 5; snout-vent length: 8.0-9.1 cm; body mass: 87-92 g) from Selleries Pond presented petechiae and dermal ulcerations on the rear limbs associated with the isolation of Aeromonas salmonicida and A. sobria. In both mortality events, the interdisciplinary approach revealed an association between frog mortalities and the isolation of bacteria. Isolated bacteria are considered opportunistic pathogens, and the high values of the water temperature has certainly led a stress on the frogs, favouring the spread of bacteria and the death of the frogs. Further studies are needed to assess the pathophysiological effects of the opportunistic bacteria here isolated, clarifying the interactions between emerging pathogens and climate change.
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Affiliation(s)
- Paolo Pastorino
- Istituto Zooprofilattico Sperimentale Del Piemonte, Liguria e Valle D'Aosta, Via Bologna 148, 10154, Torino, Italy.
| | - Silvia Colussi
- Istituto Zooprofilattico Sperimentale Del Piemonte, Liguria e Valle D'Aosta, Via Bologna 148, 10154, Torino, Italy
| | - Katia Varello
- Istituto Zooprofilattico Sperimentale Del Piemonte, Liguria e Valle D'Aosta, Via Bologna 148, 10154, Torino, Italy
| | - Arianna Meletiadis
- Istituto Zooprofilattico Sperimentale Del Piemonte, Liguria e Valle D'Aosta, Via Bologna 148, 10154, Torino, Italy
| | - Silvia Alberti
- Ente di Gestione Delle Aree Protette Delle Alpi Cozie, Via Fransuà Fontan 1,10050, Salbertrand, Torino, Italy
| | - Alessia Di Blasio
- Azienda Sanitaria Locale TO3, ASL-TO3, Via Poirino 9, 10064, Pinerolo, Torino, Italy
| | - Giovanni Tedde
- Azienda Sanitaria Locale TO3, ASL-TO3, Via Poirino 9, 10064, Pinerolo, Torino, Italy
| | - Mattia Begovoeva
- Istituto Zooprofilattico Sperimentale Del Piemonte, Liguria e Valle D'Aosta, Via Bologna 148, 10154, Torino, Italy; European Commission for the Control of Foot-and-Mouth Disease, Food and Agriculture Organization of the United Nations, Viale Delle Terme di Caracalla, 00153, Roma, Italy
| | - Andrea Peano
- Dipartimento di Science Veterinarie, Università Degli Studi di Torino, Largo P. Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Luca Rossi
- Dipartimento di Science Veterinarie, Università Degli Studi di Torino, Largo P. Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Monia Renzi
- Dipartimento di Scienze Della Vita, Università Degli Studi di Trieste, Via L. Giorgieri 10, 34127, Trieste, Italy
| | - Pier Luigi Acutis
- Istituto Zooprofilattico Sperimentale Del Piemonte, Liguria e Valle D'Aosta, Via Bologna 148, 10154, Torino, Italy
| | - Damià Barceló
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), 08034, Barcelona, Spain; Catalan Institute for Water Research (ICRA-CERCA), 17003, Girona, Spain
| | - Marino Prearo
- Istituto Zooprofilattico Sperimentale Del Piemonte, Liguria e Valle D'Aosta, Via Bologna 148, 10154, Torino, Italy
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Population Subdivision in the Gopher Frog (Rana capito) across the Fragmented Longleaf Pine-Wiregrass Savanna of the Southeastern USA. DIVERSITY 2023. [DOI: 10.3390/d15010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Delineating genetically distinct population segments of threatened species and quantifying population connectivity are important steps in developing effective conservation and management strategies aimed at preventing extinction. The gopher frog (Rana capito) is a xeric-adapted, pond-breeding species endemic to the Gulf and Atlantic coastal plains of the southeastern United States. This species has experienced extensive habitat loss and fragmentation in the formerly widespread longleaf pine-wiregrass savanna where it lives, resulting in individual abundance declines and population extinctions throughout its range. We used individual-based clustering methods along with Bayesian inference of historical migration based on almost 1500 multilocus microsatellite genotypes to examine genetic structure in this taxon. Clustering analyses identified panhandle and peninsular populations in Florida as distinct genetic clusters separated by the Aucilla River, consistent with the division between the Coastal Plain and peninsular mitochondrial lineages, respectively. Analysis of historical migration indicated an east–west population divergence event followed by immigration to the east. Together, our results indicate that the genetically distinct Coastal Plain and peninsular Florida lineages should be considered separately for conservation and management purposes.
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